Prosecutors in Zhu Yufu's trial for subversion cited text messages that he sent using Skype. Photograph: Mario Tama/Getty Images

Skype, the web-based communications company, reportedly set up a secret programme to make it easier for US surveillance agencies to access customers' information.

The programme, called Project Chess and first revealed by the New York Times on Thursday, was said to have been established before Skype was bought by Microsoft in 2011. Microsoft's links with US security are under intense scrutiny following the Guardian's revelation of Prism, a surveillance program run by the National Security Agency (NSA), that claimed "direct" access to its servers and those of rivals including Apple, Facebook and Google.

Project Chess was set up to explore the legal and technical issues involved in making Skype's communications more readily available to law enforcement and security officials, according to the Times. Only a handful of executives were aware of the plan. The company did not immediately return a call for comment.

Last year Skype denied reports that it had changed its software following the Microsoft acquisition in order to allow law enforcement easier access to communications. "Nothing could be more contrary to the Skype philosophy," Mark Gillett, vice president of Microsoft's Skype division, said in a blog post.

According to the Prism documents, Skype had been co-operating with the NSA's scheme since February 2011, eight months before the software giant took it over. The document gives little detail on the technical nature of that cooperation. Microsoft declined to comment.

The news comes as the tech firms are attempting to distance themselves from the Prism revelations. All the firm's listed as participating in the Prism scheme have denied that they give the NSA "direct" access to their servers, as claimed by the slide presentation, and said that they only comply with legal requests made through the courts.

But since the story broke a more nuanced picture of how the tech firms work with the surveillance authorities has emerged. The US authorities have become increasingly interested in tech firms and its employees after initially struggling to keep up with the shift to digital communications. NSA officials have held high level talks with executives in the tech firms and are actively recruiting in the tech community.

'That information is how they make their money'

Shane Harris, author of The Watchers: The Rise of America's Surveillance State, said the NSA had a crisis in the late 1990s when it realised communication was increasingly digital and it was falling behind in its powers to track that data. "You can not overstate that without this data the NSA would be blind," he said.

The NSA employs former valley executives, including Max Kelly, the former chief security officer for Facebook, and has increasingly sought to hire people in the hacker community. Former NSA director lieutenant general Kenneth Minihan has taken the opposite tack and is helping create the next generation of tech security firms. Minihan is managing director of Paladin Capital, a private equity firm that has a fund dedicated to investing in homeland security. Paladin also employs Dr Alf Andreassen, a former technical adviser for naval warfare who was also for classified national programmes at AT&T and Bell Laboratories.

Harris said the ties were only likely to deepen as technology moves ever more of our communications on line. He warned the move was likely to present more problems for the tech firms as their consumers worry about their privacy. "It's been fascinating for me listening to the push back from the tech companies," said Harris.

Christopher Soghoian, a senior policy analyst studying technological surveillance at the American Civil Liberties Union, said the relationship between the tech giants and the NSA has a fundamental – and ironic – flaw that guarantees the Prism scandal is unlikely to be the last time tensions surface between the two.

The US spying apparatus and Silicon Valley's top tech firms are basically in the same business, collecting information on people, he said. "It's a weird symbiotic relationship. It's not that Facebook and Google are trying to build a surveillance system but they effectively have," he said. "If they wanted to, Google and Facebook could use technology to tackle the issue, anonymizing and deleting their customers' information. But that information is how they make their money, so that is never going to happen."